Certain National Cancer Institute protocol patients are imaged repetitively over the course of many days or weeks. For several reasons, it is desirable to () align the images from one imaging session to another and (2) align the two-dimensional nuclear medicine projection images with computed tomography (CT) images of the same subject. Alignment of projection images from one imaging session to another permits more accurate quantitation of changes in uptake over time. Aligning scans done on subsequent days also permits a single transmission scan to be used to perform absolute quantitation. Alignment of the nuclear medicine projection images with CT data permits correlation of radiopharmaceutical uptake with morphological structure. In addition, the CT data may themselves be used to perform attenuation correction of the emission data. An investigation of alignment scheme (1) has been performed, using an adaptation of a technique previously published by our group for three-dimensional alignment of PET data. The method was modified for alignment of two-dimensional projection images and uses maximal pixel-to-pixel correlation techniques, applied to the transmission scan. The method uses lung borders to optimize the alignment. The method has now been thoroughly tested on phantoms and with simulated and actual motion-of-patient data. A manuscript is being prepared for publication. In addition, a computer program has been written to allow the physician to point to a region of interest on the emission data and automatically display the corresponding CT slice.